DreINT0121669 @ danRer10
Intron Retention
Gene
ENSDARG00000004539 | ptgs2a
Description
prostaglandin-endoperoxide synthase 2a [Source:ZFIN;Acc:ZDB-GENE-020530-2]
Coordinates
chr2:21265435-21265802:-
Coord C1 exon
chr2:21265674-21265802
Coord A exon
chr2:21265552-21265673
Coord C2 exon
chr2:21265435-21265551
Length
122 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TATGGCTTTTTTATTTGCAGACG
3' ss Score
9.93
Exon sequences
Seq C1 exon
AATACAACGGGCTCGACCAGAGTAACGCATCTCTGCTTCAACAGCCTCTAGATAATAACACTTCTGGAATGAATAAACTGGTTTGCTTGGTCCTACTTTCAAGCATTTGGATCTTTCCTGGTGAAGGAT
Seq A exon
GTAAGTTAAAACAAATTTACTCTGTTAGACAGACCTGCTTCTGTGAATTGTTCTACTCAAATGCAGTCTAATAATGCCTGGGACAAACATTCAATTTTCCTTTATGGCTTTTTTATTTGCAG
Seq C2 exon
ACGACCCTTGCTGTGCACAGCCTTGCCAAAACCAGGGCGTGTGTTTATCCAAGGGAGCTGATGCTTATGAATGTGACTGCACCAGGACAGGATATTATGGTGAAAACTGCACTACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004539:ENSDART00000006870:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=82.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATACAACGGGCTCGACCAGA
R:
GGGTAGTGCAGTTTTCACCAT
Band lengths:
246-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]